1 Data preparation

1.1 Outline

  • Load scripts: loads libraries and useful scripts used in the analyses; all .R files contained in scripts at the root of the factory are automatically loaded

  • Load data: imports datasets, and may contain some ad hoc changes to the data such as specific data cleaning (not used in other reports), new variables used in the analyses, etc.

1.2 Load packages


library(reportfactory)
library(here)
library(rio) 
library(tidyverse)
library(incidence)
library(distcrete)
library(epitrix)
library(earlyR)
library(projections)
library(linelist)
library(remotes)
library(janitor)
library(kableExtra)
library(DT)
library(cyphr)
library(chngpt)
library(lubridate)
library(ggpubr)
library(ggnewscale)

1.3 Load scripts

These scripts will load:

  • all scripts stored as .R files inside /scripts/
  • all scripts stored as .R files inside /src/

These scripts also contain routines to access the latest clean encrypted data (see next section).


reportfactory::rfh_load_scripts()

1.4 Load clean data

We import the latest NHS pathways data:


x <- import_pathways() %>%
  as_tibble()
x
## # A tibble: 235,461 x 11
##    site_type date       sex   age   ccg_code ccg_name count postcode nhs_region
##    <chr>     <date>     <chr> <chr> <chr>    <chr>    <int> <chr>    <chr>     
##  1 111       2020-03-18 fema… miss… e380000… nhs_glo…     1 gl34fe   South West
##  2 111       2020-03-18 fema… miss… e380001… nhs_sou…     1 ne325nn  North Eas…
##  3 111       2020-03-18 fema… 0-18  e380000… nhs_air…     8 bd57jr   North Eas…
##  4 111       2020-03-18 fema… 0-18  e380000… nhs_ash…     7 tn254ab  South East
##  5 111       2020-03-18 fema… 0-18  e380000… nhs_bar…    35 rm13ae   London    
##  6 111       2020-03-18 fema… 0-18  e380000… nhs_bar…     9 n111np   London    
##  7 111       2020-03-18 fema… 0-18  e380000… nhs_bar…    11 s752py   North Eas…
##  8 111       2020-03-18 fema… 0-18  e380000… nhs_bas…    19 ss143hg  East of E…
##  9 111       2020-03-18 fema… 0-18  e380000… nhs_bas…     6 dn227xf  North Eas…
## 10 111       2020-03-18 fema… 0-18  e380000… nhs_bat…     9 ba25rp   South West
## # … with 235,451 more rows, and 2 more variables: day <int>, weekday <fct>

We also import demographics data for NHS regions in England, used later in our analysis:


path <- here::here("data", "csv", "nhs_region_population_2018.csv")
nhs_region_pop <- rio::import(path) %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

nhs_region_pop$nhs_region <- gsub(" Of ", " of ", nhs_region_pop$nhs_region)
nhs_region_pop$nhs_region <- gsub(" And ", " and ", nhs_region_pop$nhs_region)
nhs_region_pop
##                  nhs_region variable      value
## 1                North West     0-18 0.22538599
## 2  North East and Yorkshire     0-18 0.21876449
## 3                  Midlands     0-18 0.22564656
## 4           East of England     0-18 0.22810783
## 5                    London     0-18 0.23764782
## 6                South East     0-18 0.22458811
## 7                South West     0-18 0.20799797
## 8                North West    19-69 0.64274078
## 9  North East and Yorkshire    19-69 0.64437753
## 10                 Midlands    19-69 0.63876675
## 11          East of England    19-69 0.63034229
## 12                   London    19-69 0.67820084
## 13               South East    19-69 0.63267336
## 14               South West    19-69 0.63176131
## 15               North West   70-120 0.13187323
## 16 North East and Yorkshire   70-120 0.13685797
## 17                 Midlands   70-120 0.13558669
## 18          East of England   70-120 0.14154988
## 19                   London   70-120 0.08415135
## 20               South East   70-120 0.14273853
## 21               South West   70-120 0.16024072

Finally, we import publically available deaths per NHS region:


dth <- import_deaths() %>%
  mutate(nhs_region = str_to_title(gsub("_"," ",nhs_region)))

#truncation to account for reporting delay
delay_max <- 21

dth$nhs_region <- gsub(" Of ", " of ", dth$nhs_region)
dth$nhs_region <- gsub(" And ", " and ", dth$nhs_region)
dth
##      date_report               nhs_region deaths
## 1     2020-03-01          East of England      0
## 2     2020-03-02          East of England      1
## 3     2020-03-03          East of England      0
## 4     2020-03-04          East of England      0
## 5     2020-03-05          East of England      0
## 6     2020-03-06          East of England      1
## 7     2020-03-07          East of England      0
## 8     2020-03-08          East of England      0
## 9     2020-03-09          East of England      1
## 10    2020-03-10          East of England      0
## 11    2020-03-11          East of England      0
## 12    2020-03-12          East of England      0
## 13    2020-03-13          East of England      1
## 14    2020-03-14          East of England      2
## 15    2020-03-15          East of England      2
## 16    2020-03-16          East of England      1
## 17    2020-03-17          East of England      1
## 18    2020-03-18          East of England      5
## 19    2020-03-19          East of England      4
## 20    2020-03-20          East of England      2
## 21    2020-03-21          East of England     11
## 22    2020-03-22          East of England     12
## 23    2020-03-23          East of England     11
## 24    2020-03-24          East of England     19
## 25    2020-03-25          East of England     26
## 26    2020-03-26          East of England     36
## 27    2020-03-27          East of England     38
## 28    2020-03-28          East of England     28
## 29    2020-03-29          East of England     43
## 30    2020-03-30          East of England     45
## 31    2020-03-31          East of England     70
## 32    2020-04-01          East of England     62
## 33    2020-04-02          East of England     65
## 34    2020-04-03          East of England     80
## 35    2020-04-04          East of England     71
## 36    2020-04-05          East of England     76
## 37    2020-04-06          East of England     71
## 38    2020-04-07          East of England     93
## 39    2020-04-08          East of England    111
## 40    2020-04-09          East of England     87
## 41    2020-04-10          East of England     74
## 42    2020-04-11          East of England     92
## 43    2020-04-12          East of England    100
## 44    2020-04-13          East of England     78
## 45    2020-04-14          East of England     61
## 46    2020-04-15          East of England     82
## 47    2020-04-16          East of England     74
## 48    2020-04-17          East of England     86
## 49    2020-04-18          East of England     64
## 50    2020-04-19          East of England     67
## 51    2020-04-20          East of England     67
## 52    2020-04-21          East of England     75
## 53    2020-04-22          East of England     67
## 54    2020-04-23          East of England     49
## 55    2020-04-24          East of England     66
## 56    2020-04-25          East of England     54
## 57    2020-04-26          East of England     48
## 58    2020-04-27          East of England     46
## 59    2020-04-28          East of England     58
## 60    2020-04-29          East of England     32
## 61    2020-04-30          East of England     45
## 62    2020-05-01          East of England     49
## 63    2020-05-02          East of England     29
## 64    2020-05-03          East of England     41
## 65    2020-05-04          East of England     19
## 66    2020-05-05          East of England     36
## 67    2020-05-06          East of England     31
## 68    2020-05-07          East of England     33
## 69    2020-05-08          East of England     33
## 70    2020-05-09          East of England     29
## 71    2020-05-10          East of England     22
## 72    2020-05-11          East of England     18
## 73    2020-05-12          East of England     21
## 74    2020-05-13          East of England     27
## 75    2020-05-14          East of England     26
## 76    2020-05-15          East of England     19
## 77    2020-05-16          East of England     26
## 78    2020-05-17          East of England     17
## 79    2020-05-18          East of England     25
## 80    2020-05-19          East of England     15
## 81    2020-05-20          East of England     26
## 82    2020-05-21          East of England     21
## 83    2020-05-22          East of England     13
## 84    2020-05-23          East of England     12
## 85    2020-05-24          East of England     17
## 86    2020-05-25          East of England     25
## 87    2020-05-26          East of England     14
## 88    2020-05-27          East of England     12
## 89    2020-05-28          East of England     17
## 90    2020-05-29          East of England     16
## 91    2020-05-30          East of England      9
## 92    2020-05-31          East of England      8
## 93    2020-06-01          East of England     17
## 94    2020-06-02          East of England     14
## 95    2020-06-03          East of England     10
## 96    2020-06-04          East of England      7
## 97    2020-06-05          East of England     14
## 98    2020-06-06          East of England      5
## 99    2020-06-07          East of England      9
## 100   2020-06-08          East of England      7
## 101   2020-06-09          East of England      6
## 102   2020-06-10          East of England      8
## 103   2020-06-11          East of England      1
## 104   2020-06-12          East of England      9
## 105   2020-06-13          East of England      5
## 106   2020-06-14          East of England      4
## 107   2020-06-15          East of England      8
## 108   2020-06-16          East of England      3
## 109   2020-06-17          East of England      7
## 110   2020-06-18          East of England      4
## 111   2020-06-19          East of England      7
## 112   2020-06-20          East of England      4
## 113   2020-06-21          East of England      3
## 114   2020-06-22          East of England      6
## 115   2020-06-23          East of England      5
## 116   2020-06-24          East of England      4
## 117   2020-06-25          East of England      1
## 118   2020-06-26          East of England      5
## 119   2020-06-27          East of England      6
## 120   2020-06-28          East of England      8
## 121   2020-06-29          East of England      4
## 122   2020-06-30          East of England      5
## 123   2020-07-01          East of England      2
## 124   2020-07-02          East of England      5
## 125   2020-07-03          East of England      0
## 126   2020-07-04          East of England      3
## 127   2020-07-05          East of England      1
## 128   2020-07-06          East of England      2
## 129   2020-07-07          East of England      2
## 130   2020-07-08          East of England      0
## 131   2020-07-09          East of England      8
## 132   2020-07-10          East of England      4
## 133   2020-07-11          East of England      2
## 134   2020-07-12          East of England      1
## 135   2020-07-13          East of England      8
## 136   2020-07-14          East of England      2
## 137   2020-07-15          East of England      0
## 138   2020-07-16          East of England      0
## 139   2020-07-17          East of England      0
## 140   2020-07-18          East of England      0
## 141   2020-07-19          East of England      1
## 142   2020-07-20          East of England      1
## 143   2020-07-21          East of England      1
## 144   2020-07-22          East of England      2
## 145   2020-07-23          East of England      1
## 146   2020-07-24          East of England      1
## 147   2020-07-25          East of England      0
## 148   2020-07-26          East of England      1
## 149   2020-07-27          East of England      1
## 150   2020-07-28          East of England      2
## 151   2020-07-29          East of England      0
## 152   2020-07-30          East of England      0
## 153   2020-07-31          East of England      1
## 154   2020-08-01          East of England      0
## 155   2020-08-02          East of England      0
## 156   2020-08-03          East of England      0
## 157   2020-08-04          East of England      1
## 158   2020-08-05          East of England      1
## 159   2020-08-06          East of England      0
## 160   2020-08-07          East of England      1
## 161   2020-08-08          East of England      0
## 162   2020-08-09          East of England      0
## 163   2020-08-10          East of England      1
## 164   2020-08-11          East of England      2
## 165   2020-08-12          East of England      1
## 166   2020-08-13          East of England      0
## 167   2020-08-14          East of England      0
## 168   2020-08-15          East of England      1
## 169   2020-08-16          East of England      0
## 170   2020-08-17          East of England      0
## 171   2020-08-18          East of England      2
## 172   2020-08-19          East of England      1
## 173   2020-08-20          East of England      1
## 174   2020-08-21          East of England      0
## 175   2020-08-22          East of England      1
## 176   2020-08-23          East of England      1
## 177   2020-08-24          East of England      0
## 178   2020-08-25          East of England      0
## 179   2020-08-26          East of England      1
## 180   2020-08-27          East of England      1
## 181   2020-08-28          East of England      0
## 182   2020-08-29          East of England      0
## 183   2020-08-30          East of England      0
## 184   2020-08-31          East of England      0
## 185   2020-09-01          East of England      0
## 186   2020-09-02          East of England      0
## 187   2020-09-03          East of England      1
## 188   2020-09-04          East of England      1
## 189   2020-09-05          East of England      0
## 190   2020-09-06          East of England      0
## 191   2020-03-01                   London      0
## 192   2020-03-02                   London      0
## 193   2020-03-03                   London      0
## 194   2020-03-04                   London      0
## 195   2020-03-05                   London      0
## 196   2020-03-06                   London      1
## 197   2020-03-07                   London      0
## 198   2020-03-08                   London      0
## 199   2020-03-09                   London      1
## 200   2020-03-10                   London      0
## 201   2020-03-11                   London      5
## 202   2020-03-12                   London      6
## 203   2020-03-13                   London     10
## 204   2020-03-14                   London     13
## 205   2020-03-15                   London      9
## 206   2020-03-16                   London     15
## 207   2020-03-17                   London     23
## 208   2020-03-18                   London     28
## 209   2020-03-19                   London     25
## 210   2020-03-20                   London     44
## 211   2020-03-21                   London     49
## 212   2020-03-22                   London     54
## 213   2020-03-23                   London     63
## 214   2020-03-24                   London     86
## 215   2020-03-25                   London    112
## 216   2020-03-26                   London    129
## 217   2020-03-27                   London    129
## 218   2020-03-28                   London    122
## 219   2020-03-29                   London    145
## 220   2020-03-30                   London    149
## 221   2020-03-31                   London    181
## 222   2020-04-01                   London    202
## 223   2020-04-02                   London    191
## 224   2020-04-03                   London    198
## 225   2020-04-04                   London    231
## 226   2020-04-05                   London    195
## 227   2020-04-06                   London    197
## 228   2020-04-07                   London    220
## 229   2020-04-08                   London    239
## 230   2020-04-09                   London    206
## 231   2020-04-10                   London    171
## 232   2020-04-11                   London    178
## 233   2020-04-12                   London    158
## 234   2020-04-13                   London    166
## 235   2020-04-14                   London    143
## 236   2020-04-15                   London    142
## 237   2020-04-16                   London    140
## 238   2020-04-17                   London    100
## 239   2020-04-18                   London    101
## 240   2020-04-19                   London    103
## 241   2020-04-20                   London     96
## 242   2020-04-21                   London     94
## 243   2020-04-22                   London    109
## 244   2020-04-23                   London     77
## 245   2020-04-24                   London     71
## 246   2020-04-25                   London     58
## 247   2020-04-26                   London     53
## 248   2020-04-27                   London     51
## 249   2020-04-28                   London     44
## 250   2020-04-29                   London     45
## 251   2020-04-30                   London     40
## 252   2020-05-01                   London     41
## 253   2020-05-02                   London     41
## 254   2020-05-03                   London     36
## 255   2020-05-04                   London     30
## 256   2020-05-05                   London     25
## 257   2020-05-06                   London     37
## 258   2020-05-07                   London     37
## 259   2020-05-08                   London     30
## 260   2020-05-09                   London     23
## 261   2020-05-10                   London     26
## 262   2020-05-11                   London     18
## 263   2020-05-12                   London     18
## 264   2020-05-13                   London     17
## 265   2020-05-14                   London     20
## 266   2020-05-15                   London     19
## 267   2020-05-16                   London     14
## 268   2020-05-17                   London     15
## 269   2020-05-18                   London     11
## 270   2020-05-19                   London     14
## 271   2020-05-20                   London     19
## 272   2020-05-21                   London     12
## 273   2020-05-22                   London     10
## 274   2020-05-23                   London      6
## 275   2020-05-24                   London      7
## 276   2020-05-25                   London      9
## 277   2020-05-26                   London     14
## 278   2020-05-27                   London      7
## 279   2020-05-28                   London      8
## 280   2020-05-29                   London      7
## 281   2020-05-30                   London     12
## 282   2020-05-31                   London      6
## 283   2020-06-01                   London     10
## 284   2020-06-02                   London      8
## 285   2020-06-03                   London      6
## 286   2020-06-04                   London      8
## 287   2020-06-05                   London      4
## 288   2020-06-06                   London      0
## 289   2020-06-07                   London      5
## 290   2020-06-08                   London      5
## 291   2020-06-09                   London      5
## 292   2020-06-10                   London      8
## 293   2020-06-11                   London      5
## 294   2020-06-12                   London      3
## 295   2020-06-13                   London      3
## 296   2020-06-14                   London      3
## 297   2020-06-15                   London      1
## 298   2020-06-16                   London      2
## 299   2020-06-17                   London      1
## 300   2020-06-18                   London      2
## 301   2020-06-19                   London      5
## 302   2020-06-20                   London      3
## 303   2020-06-21                   London      4
## 304   2020-06-22                   London      2
## 305   2020-06-23                   London      1
## 306   2020-06-24                   London      4
## 307   2020-06-25                   London      3
## 308   2020-06-26                   London      2
## 309   2020-06-27                   London      1
## 310   2020-06-28                   London      2
## 311   2020-06-29                   London      2
## 312   2020-06-30                   London      1
## 313   2020-07-01                   London      2
## 314   2020-07-02                   London      2
## 315   2020-07-03                   London      2
## 316   2020-07-04                   London      1
## 317   2020-07-05                   London      3
## 318   2020-07-06                   London      2
## 319   2020-07-07                   London      1
## 320   2020-07-08                   London      3
## 321   2020-07-09                   London      4
## 322   2020-07-10                   London      0
## 323   2020-07-11                   London      1
## 324   2020-07-12                   London      1
## 325   2020-07-13                   London      1
## 326   2020-07-14                   London      0
## 327   2020-07-15                   London      2
## 328   2020-07-16                   London      0
## 329   2020-07-17                   London      0
## 330   2020-07-18                   London      2
## 331   2020-07-19                   London      0
## 332   2020-07-20                   London      0
## 333   2020-07-21                   London      1
## 334   2020-07-22                   London      0
## 335   2020-07-23                   London      2
## 336   2020-07-24                   London      0
## 337   2020-07-25                   London      1
## 338   2020-07-26                   London      0
## 339   2020-07-27                   London      1
## 340   2020-07-28                   London      0
## 341   2020-07-29                   London      0
## 342   2020-07-30                   London      1
## 343   2020-07-31                   London      0
## 344   2020-08-01                   London      0
## 345   2020-08-02                   London      3
## 346   2020-08-03                   London      0
## 347   2020-08-04                   London      0
## 348   2020-08-05                   London      0
## 349   2020-08-06                   London      1
## 350   2020-08-07                   London      0
## 351   2020-08-08                   London      0
## 352   2020-08-09                   London      0
## 353   2020-08-10                   London      0
## 354   2020-08-11                   London      1
## 355   2020-08-12                   London      0
## 356   2020-08-13                   London      2
## 357   2020-08-14                   London      0
## 358   2020-08-15                   London      0
## 359   2020-08-16                   London      0
## 360   2020-08-17                   London      1
## 361   2020-08-18                   London      1
## 362   2020-08-19                   London      0
## 363   2020-08-20                   London      1
## 364   2020-08-21                   London      0
## 365   2020-08-22                   London      0
## 366   2020-08-23                   London      0
## 367   2020-08-24                   London      1
## 368   2020-08-25                   London      1
## 369   2020-08-26                   London      0
## 370   2020-08-27                   London      0
## 371   2020-08-28                   London      0
## 372   2020-08-29                   London      0
## 373   2020-08-30                   London      0
## 374   2020-08-31                   London      1
## 375   2020-09-01                   London      0
## 376   2020-09-02                   London      1
## 377   2020-09-03                   London      1
## 378   2020-09-04                   London      0
## 379   2020-09-05                   London      0
## 380   2020-09-06                   London      0
## 381   2020-03-01                 Midlands      0
## 382   2020-03-02                 Midlands      0
## 383   2020-03-03                 Midlands      1
## 384   2020-03-04                 Midlands      0
## 385   2020-03-05                 Midlands      0
## 386   2020-03-06                 Midlands      0
## 387   2020-03-07                 Midlands      0
## 388   2020-03-08                 Midlands      2
## 389   2020-03-09                 Midlands      1
## 390   2020-03-10                 Midlands      0
## 391   2020-03-11                 Midlands      2
## 392   2020-03-12                 Midlands      6
## 393   2020-03-13                 Midlands      5
## 394   2020-03-14                 Midlands      4
## 395   2020-03-15                 Midlands      5
## 396   2020-03-16                 Midlands     11
## 397   2020-03-17                 Midlands      8
## 398   2020-03-18                 Midlands     13
## 399   2020-03-19                 Midlands      8
## 400   2020-03-20                 Midlands     28
## 401   2020-03-21                 Midlands     13
## 402   2020-03-22                 Midlands     31
## 403   2020-03-23                 Midlands     33
## 404   2020-03-24                 Midlands     41
## 405   2020-03-25                 Midlands     48
## 406   2020-03-26                 Midlands     64
## 407   2020-03-27                 Midlands     72
## 408   2020-03-28                 Midlands     89
## 409   2020-03-29                 Midlands     92
## 410   2020-03-30                 Midlands     90
## 411   2020-03-31                 Midlands    123
## 412   2020-04-01                 Midlands    140
## 413   2020-04-02                 Midlands    142
## 414   2020-04-03                 Midlands    124
## 415   2020-04-04                 Midlands    151
## 416   2020-04-05                 Midlands    164
## 417   2020-04-06                 Midlands    140
## 418   2020-04-07                 Midlands    123
## 419   2020-04-08                 Midlands    186
## 420   2020-04-09                 Midlands    139
## 421   2020-04-10                 Midlands    127
## 422   2020-04-11                 Midlands    142
## 423   2020-04-12                 Midlands    139
## 424   2020-04-13                 Midlands    120
## 425   2020-04-14                 Midlands    116
## 426   2020-04-15                 Midlands    147
## 427   2020-04-16                 Midlands    102
## 428   2020-04-17                 Midlands    118
## 429   2020-04-18                 Midlands    115
## 430   2020-04-19                 Midlands     92
## 431   2020-04-20                 Midlands    107
## 432   2020-04-21                 Midlands     86
## 433   2020-04-22                 Midlands     78
## 434   2020-04-23                 Midlands    103
## 435   2020-04-24                 Midlands     79
## 436   2020-04-25                 Midlands     72
## 437   2020-04-26                 Midlands     81
## 438   2020-04-27                 Midlands     74
## 439   2020-04-28                 Midlands     68
## 440   2020-04-29                 Midlands     53
## 441   2020-04-30                 Midlands     56
## 442   2020-05-01                 Midlands     64
## 443   2020-05-02                 Midlands     51
## 444   2020-05-03                 Midlands     52
## 445   2020-05-04                 Midlands     61
## 446   2020-05-05                 Midlands     59
## 447   2020-05-06                 Midlands     59
## 448   2020-05-07                 Midlands     48
## 449   2020-05-08                 Midlands     34
## 450   2020-05-09                 Midlands     37
## 451   2020-05-10                 Midlands     42
## 452   2020-05-11                 Midlands     33
## 453   2020-05-12                 Midlands     45
## 454   2020-05-13                 Midlands     40
## 455   2020-05-14                 Midlands     38
## 456   2020-05-15                 Midlands     40
## 457   2020-05-16                 Midlands     34
## 458   2020-05-17                 Midlands     31
## 459   2020-05-18                 Midlands     36
## 460   2020-05-19                 Midlands     35
## 461   2020-05-20                 Midlands     36
## 462   2020-05-21                 Midlands     32
## 463   2020-05-22                 Midlands     27
## 464   2020-05-23                 Midlands     34
## 465   2020-05-24                 Midlands     20
## 466   2020-05-25                 Midlands     26
## 467   2020-05-26                 Midlands     33
## 468   2020-05-27                 Midlands     29
## 469   2020-05-28                 Midlands     28
## 470   2020-05-29                 Midlands     20
## 471   2020-05-30                 Midlands     21
## 472   2020-05-31                 Midlands     22
## 473   2020-06-01                 Midlands     20
## 474   2020-06-02                 Midlands     22
## 475   2020-06-03                 Midlands     24
## 476   2020-06-04                 Midlands     16
## 477   2020-06-05                 Midlands     21
## 478   2020-06-06                 Midlands     20
## 479   2020-06-07                 Midlands     17
## 480   2020-06-08                 Midlands     16
## 481   2020-06-09                 Midlands     18
## 482   2020-06-10                 Midlands     15
## 483   2020-06-11                 Midlands     13
## 484   2020-06-12                 Midlands     12
## 485   2020-06-13                 Midlands      6
## 486   2020-06-14                 Midlands     18
## 487   2020-06-15                 Midlands     12
## 488   2020-06-16                 Midlands     15
## 489   2020-06-17                 Midlands     11
## 490   2020-06-18                 Midlands     15
## 491   2020-06-19                 Midlands     10
## 492   2020-06-20                 Midlands     15
## 493   2020-06-21                 Midlands     14
## 494   2020-06-22                 Midlands     14
## 495   2020-06-23                 Midlands     16
## 496   2020-06-24                 Midlands     15
## 497   2020-06-25                 Midlands     18
## 498   2020-06-26                 Midlands      5
## 499   2020-06-27                 Midlands      5
## 500   2020-06-28                 Midlands      7
## 501   2020-06-29                 Midlands      6
## 502   2020-06-30                 Midlands      6
## 503   2020-07-01                 Midlands      7
## 504   2020-07-02                 Midlands     10
## 505   2020-07-03                 Midlands      3
## 506   2020-07-04                 Midlands      4
## 507   2020-07-05                 Midlands      6
## 508   2020-07-06                 Midlands      5
## 509   2020-07-07                 Midlands      3
## 510   2020-07-08                 Midlands      5
## 511   2020-07-09                 Midlands      9
## 512   2020-07-10                 Midlands      3
## 513   2020-07-11                 Midlands      0
## 514   2020-07-12                 Midlands      5
## 515   2020-07-13                 Midlands      1
## 516   2020-07-14                 Midlands      1
## 517   2020-07-15                 Midlands      6
## 518   2020-07-16                 Midlands      2
## 519   2020-07-17                 Midlands      3
## 520   2020-07-18                 Midlands      3
## 521   2020-07-19                 Midlands      3
## 522   2020-07-20                 Midlands      3
## 523   2020-07-21                 Midlands      1
## 524   2020-07-22                 Midlands      2
## 525   2020-07-23                 Midlands      6
## 526   2020-07-24                 Midlands      1
## 527   2020-07-25                 Midlands      4
## 528   2020-07-26                 Midlands      4
## 529   2020-07-27                 Midlands      5
## 530   2020-07-28                 Midlands      1
## 531   2020-07-29                 Midlands      1
## 532   2020-07-30                 Midlands      1
## 533   2020-07-31                 Midlands      2
## 534   2020-08-01                 Midlands      0
## 535   2020-08-02                 Midlands      1
## 536   2020-08-03                 Midlands      2
## 537   2020-08-04                 Midlands      1
## 538   2020-08-05                 Midlands      1
## 539   2020-08-06                 Midlands      0
## 540   2020-08-07                 Midlands      3
## 541   2020-08-08                 Midlands      2
## 542   2020-08-09                 Midlands      0
## 543   2020-08-10                 Midlands      0
## 544   2020-08-11                 Midlands      2
## 545   2020-08-12                 Midlands      0
## 546   2020-08-13                 Midlands      0
## 547   2020-08-14                 Midlands      0
## 548   2020-08-15                 Midlands      1
## 549   2020-08-16                 Midlands      0
## 550   2020-08-17                 Midlands      0
## 551   2020-08-18                 Midlands      0
## 552   2020-08-19                 Midlands      0
## 553   2020-08-20                 Midlands      0
## 554   2020-08-21                 Midlands      1
## 555   2020-08-22                 Midlands      0
## 556   2020-08-23                 Midlands      0
## 557   2020-08-24                 Midlands      0
## 558   2020-08-25                 Midlands      2
## 559   2020-08-26                 Midlands      3
## 560   2020-08-27                 Midlands      2
## 561   2020-08-28                 Midlands      1
## 562   2020-08-29                 Midlands      0
## 563   2020-08-30                 Midlands      1
## 564   2020-08-31                 Midlands      1
## 565   2020-09-01                 Midlands      0
## 566   2020-09-02                 Midlands      2
## 567   2020-09-03                 Midlands      0
## 568   2020-09-04                 Midlands      0
## 569   2020-09-05                 Midlands      0
## 570   2020-09-06                 Midlands      0
## 571   2020-03-01 North East and Yorkshire      0
## 572   2020-03-02 North East and Yorkshire      0
## 573   2020-03-03 North East and Yorkshire      0
## 574   2020-03-04 North East and Yorkshire      0
## 575   2020-03-05 North East and Yorkshire      0
## 576   2020-03-06 North East and Yorkshire      0
## 577   2020-03-07 North East and Yorkshire      0
## 578   2020-03-08 North East and Yorkshire      0
## 579   2020-03-09 North East and Yorkshire      0
## 580   2020-03-10 North East and Yorkshire      0
## 581   2020-03-11 North East and Yorkshire      0
## 582   2020-03-12 North East and Yorkshire      0
## 583   2020-03-13 North East and Yorkshire      0
## 584   2020-03-14 North East and Yorkshire      0
## 585   2020-03-15 North East and Yorkshire      2
## 586   2020-03-16 North East and Yorkshire      3
## 587   2020-03-17 North East and Yorkshire      1
## 588   2020-03-18 North East and Yorkshire      2
## 589   2020-03-19 North East and Yorkshire      6
## 590   2020-03-20 North East and Yorkshire      5
## 591   2020-03-21 North East and Yorkshire      6
## 592   2020-03-22 North East and Yorkshire      7
## 593   2020-03-23 North East and Yorkshire      9
## 594   2020-03-24 North East and Yorkshire      8
## 595   2020-03-25 North East and Yorkshire     18
## 596   2020-03-26 North East and Yorkshire     21
## 597   2020-03-27 North East and Yorkshire     28
## 598   2020-03-28 North East and Yorkshire     35
## 599   2020-03-29 North East and Yorkshire     38
## 600   2020-03-30 North East and Yorkshire     64
## 601   2020-03-31 North East and Yorkshire     60
## 602   2020-04-01 North East and Yorkshire     67
## 603   2020-04-02 North East and Yorkshire     75
## 604   2020-04-03 North East and Yorkshire    100
## 605   2020-04-04 North East and Yorkshire    105
## 606   2020-04-05 North East and Yorkshire     92
## 607   2020-04-06 North East and Yorkshire     96
## 608   2020-04-07 North East and Yorkshire    102
## 609   2020-04-08 North East and Yorkshire    107
## 610   2020-04-09 North East and Yorkshire    111
## 611   2020-04-10 North East and Yorkshire    117
## 612   2020-04-11 North East and Yorkshire     98
## 613   2020-04-12 North East and Yorkshire     84
## 614   2020-04-13 North East and Yorkshire     94
## 615   2020-04-14 North East and Yorkshire    107
## 616   2020-04-15 North East and Yorkshire     96
## 617   2020-04-16 North East and Yorkshire    103
## 618   2020-04-17 North East and Yorkshire     88
## 619   2020-04-18 North East and Yorkshire     95
## 620   2020-04-19 North East and Yorkshire     88
## 621   2020-04-20 North East and Yorkshire    100
## 622   2020-04-21 North East and Yorkshire     76
## 623   2020-04-22 North East and Yorkshire     84
## 624   2020-04-23 North East and Yorkshire     63
## 625   2020-04-24 North East and Yorkshire     72
## 626   2020-04-25 North East and Yorkshire     69
## 627   2020-04-26 North East and Yorkshire     65
## 628   2020-04-27 North East and Yorkshire     65
## 629   2020-04-28 North East and Yorkshire     57
## 630   2020-04-29 North East and Yorkshire     69
## 631   2020-04-30 North East and Yorkshire     57
## 632   2020-05-01 North East and Yorkshire     64
## 633   2020-05-02 North East and Yorkshire     48
## 634   2020-05-03 North East and Yorkshire     40
## 635   2020-05-04 North East and Yorkshire     49
## 636   2020-05-05 North East and Yorkshire     40
## 637   2020-05-06 North East and Yorkshire     51
## 638   2020-05-07 North East and Yorkshire     45
## 639   2020-05-08 North East and Yorkshire     42
## 640   2020-05-09 North East and Yorkshire     44
## 641   2020-05-10 North East and Yorkshire     40
## 642   2020-05-11 North East and Yorkshire     29
## 643   2020-05-12 North East and Yorkshire     27
## 644   2020-05-13 North East and Yorkshire     28
## 645   2020-05-14 North East and Yorkshire     31
## 646   2020-05-15 North East and Yorkshire     32
## 647   2020-05-16 North East and Yorkshire     35
## 648   2020-05-17 North East and Yorkshire     26
## 649   2020-05-18 North East and Yorkshire     30
## 650   2020-05-19 North East and Yorkshire     27
## 651   2020-05-20 North East and Yorkshire     22
## 652   2020-05-21 North East and Yorkshire     33
## 653   2020-05-22 North East and Yorkshire     22
## 654   2020-05-23 North East and Yorkshire     18
## 655   2020-05-24 North East and Yorkshire     26
## 656   2020-05-25 North East and Yorkshire     21
## 657   2020-05-26 North East and Yorkshire     21
## 658   2020-05-27 North East and Yorkshire     22
## 659   2020-05-28 North East and Yorkshire     21
## 660   2020-05-29 North East and Yorkshire     25
## 661   2020-05-30 North East and Yorkshire     20
## 662   2020-05-31 North East and Yorkshire     20
## 663   2020-06-01 North East and Yorkshire     17
## 664   2020-06-02 North East and Yorkshire     23
## 665   2020-06-03 North East and Yorkshire     23
## 666   2020-06-04 North East and Yorkshire     17
## 667   2020-06-05 North East and Yorkshire     18
## 668   2020-06-06 North East and Yorkshire     21
## 669   2020-06-07 North East and Yorkshire     14
## 670   2020-06-08 North East and Yorkshire     11
## 671   2020-06-09 North East and Yorkshire     12
## 672   2020-06-10 North East and Yorkshire     19
## 673   2020-06-11 North East and Yorkshire      7
## 674   2020-06-12 North East and Yorkshire      9
## 675   2020-06-13 North East and Yorkshire     10
## 676   2020-06-14 North East and Yorkshire     11
## 677   2020-06-15 North East and Yorkshire      9
## 678   2020-06-16 North East and Yorkshire     10
## 679   2020-06-17 North East and Yorkshire      9
## 680   2020-06-18 North East and Yorkshire     11
## 681   2020-06-19 North East and Yorkshire      6
## 682   2020-06-20 North East and Yorkshire      5
## 683   2020-06-21 North East and Yorkshire      4
## 684   2020-06-22 North East and Yorkshire      7
## 685   2020-06-23 North East and Yorkshire      8
## 686   2020-06-24 North East and Yorkshire     10
## 687   2020-06-25 North East and Yorkshire      4
## 688   2020-06-26 North East and Yorkshire      8
## 689   2020-06-27 North East and Yorkshire      4
## 690   2020-06-28 North East and Yorkshire      5
## 691   2020-06-29 North East and Yorkshire      2
## 692   2020-06-30 North East and Yorkshire      7
## 693   2020-07-01 North East and Yorkshire      1
## 694   2020-07-02 North East and Yorkshire      4
## 695   2020-07-03 North East and Yorkshire      4
## 696   2020-07-04 North East and Yorkshire      4
## 697   2020-07-05 North East and Yorkshire      3
## 698   2020-07-06 North East and Yorkshire      2
## 699   2020-07-07 North East and Yorkshire      3
## 700   2020-07-08 North East and Yorkshire      3
## 701   2020-07-09 North East and Yorkshire      0
## 702   2020-07-10 North East and Yorkshire      3
## 703   2020-07-11 North East and Yorkshire      1
## 704   2020-07-12 North East and Yorkshire      4
## 705   2020-07-13 North East and Yorkshire      1
## 706   2020-07-14 North East and Yorkshire      1
## 707   2020-07-15 North East and Yorkshire      2
## 708   2020-07-16 North East and Yorkshire      3
## 709   2020-07-17 North East and Yorkshire      1
## 710   2020-07-18 North East and Yorkshire      2
## 711   2020-07-19 North East and Yorkshire      2
## 712   2020-07-20 North East and Yorkshire      1
## 713   2020-07-21 North East and Yorkshire      1
## 714   2020-07-22 North East and Yorkshire      6
## 715   2020-07-23 North East and Yorkshire      0
## 716   2020-07-24 North East and Yorkshire      1
## 717   2020-07-25 North East and Yorkshire      5
## 718   2020-07-26 North East and Yorkshire      1
## 719   2020-07-27 North East and Yorkshire      0
## 720   2020-07-28 North East and Yorkshire      2
## 721   2020-07-29 North East and Yorkshire      1
## 722   2020-07-30 North East and Yorkshire      0
## 723   2020-07-31 North East and Yorkshire      1
## 724   2020-08-01 North East and Yorkshire      3
## 725   2020-08-02 North East and Yorkshire      2
## 726   2020-08-03 North East and Yorkshire      1
## 727   2020-08-04 North East and Yorkshire      2
## 728   2020-08-05 North East and Yorkshire      1
## 729   2020-08-06 North East and Yorkshire      4
## 730   2020-08-07 North East and Yorkshire      0
## 731   2020-08-08 North East and Yorkshire      1
## 732   2020-08-09 North East and Yorkshire      2
## 733   2020-08-10 North East and Yorkshire      2
## 734   2020-08-11 North East and Yorkshire      2
## 735   2020-08-12 North East and Yorkshire      2
## 736   2020-08-13 North East and Yorkshire      0
## 737   2020-08-14 North East and Yorkshire      1
## 738   2020-08-15 North East and Yorkshire      1
## 739   2020-08-16 North East and Yorkshire      0
## 740   2020-08-17 North East and Yorkshire      4
## 741   2020-08-18 North East and Yorkshire      1
## 742   2020-08-19 North East and Yorkshire      0
## 743   2020-08-20 North East and Yorkshire      0
## 744   2020-08-21 North East and Yorkshire      1
## 745   2020-08-22 North East and Yorkshire      1
## 746   2020-08-23 North East and Yorkshire      2
## 747   2020-08-24 North East and Yorkshire      0
## 748   2020-08-25 North East and Yorkshire      1
## 749   2020-08-26 North East and Yorkshire      2
## 750   2020-08-27 North East and Yorkshire      1
## 751   2020-08-28 North East and Yorkshire      0
## 752   2020-08-29 North East and Yorkshire      1
## 753   2020-08-30 North East and Yorkshire      0
## 754   2020-08-31 North East and Yorkshire      0
## 755   2020-09-01 North East and Yorkshire      2
## 756   2020-09-02 North East and Yorkshire      3
## 757   2020-09-03 North East and Yorkshire      0
## 758   2020-09-04 North East and Yorkshire      0
## 759   2020-09-05 North East and Yorkshire      2
## 760   2020-09-06 North East and Yorkshire      0
## 761   2020-03-01               North West      0
## 762   2020-03-02               North West      0
## 763   2020-03-03               North West      0
## 764   2020-03-04               North West      0
## 765   2020-03-05               North West      1
## 766   2020-03-06               North West      0
## 767   2020-03-07               North West      0
## 768   2020-03-08               North West      1
## 769   2020-03-09               North West      0
## 770   2020-03-10               North West      0
## 771   2020-03-11               North West      0
## 772   2020-03-12               North West      2
## 773   2020-03-13               North West      3
## 774   2020-03-14               North West      1
## 775   2020-03-15               North West      4
## 776   2020-03-16               North West      2
## 777   2020-03-17               North West      4
## 778   2020-03-18               North West      6
## 779   2020-03-19               North West      7
## 780   2020-03-20               North West     10
## 781   2020-03-21               North West     11
## 782   2020-03-22               North West     13
## 783   2020-03-23               North West     15
## 784   2020-03-24               North West     21
## 785   2020-03-25               North West     21
## 786   2020-03-26               North West     29
## 787   2020-03-27               North West     36
## 788   2020-03-28               North West     28
## 789   2020-03-29               North West     46
## 790   2020-03-30               North West     67
## 791   2020-03-31               North West     52
## 792   2020-04-01               North West     86
## 793   2020-04-02               North West     96
## 794   2020-04-03               North West     95
## 795   2020-04-04               North West     98
## 796   2020-04-05               North West    102
## 797   2020-04-06               North West    100
## 798   2020-04-07               North West    135
## 799   2020-04-08               North West    127
## 800   2020-04-09               North West    119
## 801   2020-04-10               North West    117
## 802   2020-04-11               North West    138
## 803   2020-04-12               North West    125
## 804   2020-04-13               North West    129
## 805   2020-04-14               North West    131
## 806   2020-04-15               North West    114
## 807   2020-04-16               North West    135
## 808   2020-04-17               North West     98
## 809   2020-04-18               North West    113
## 810   2020-04-19               North West     71
## 811   2020-04-20               North West     83
## 812   2020-04-21               North West     76
## 813   2020-04-22               North West     86
## 814   2020-04-23               North West     85
## 815   2020-04-24               North West     66
## 816   2020-04-25               North West     66
## 817   2020-04-26               North West     55
## 818   2020-04-27               North West     54
## 819   2020-04-28               North West     57
## 820   2020-04-29               North West     63
## 821   2020-04-30               North West     59
## 822   2020-05-01               North West     45
## 823   2020-05-02               North West     56
## 824   2020-05-03               North West     55
## 825   2020-05-04               North West     48
## 826   2020-05-05               North West     48
## 827   2020-05-06               North West     44
## 828   2020-05-07               North West     49
## 829   2020-05-08               North West     42
## 830   2020-05-09               North West     31
## 831   2020-05-10               North West     42
## 832   2020-05-11               North West     35
## 833   2020-05-12               North West     38
## 834   2020-05-13               North West     25
## 835   2020-05-14               North West     26
## 836   2020-05-15               North West     33
## 837   2020-05-16               North West     32
## 838   2020-05-17               North West     24
## 839   2020-05-18               North West     31
## 840   2020-05-19               North West     35
## 841   2020-05-20               North West     27
## 842   2020-05-21               North West     27
## 843   2020-05-22               North West     26
## 844   2020-05-23               North West     31
## 845   2020-05-24               North West     26
## 846   2020-05-25               North West     31
## 847   2020-05-26               North West     27
## 848   2020-05-27               North West     27
## 849   2020-05-28               North West     28
## 850   2020-05-29               North West     20
## 851   2020-05-30               North West     19
## 852   2020-05-31               North West     13
## 853   2020-06-01               North West     12
## 854   2020-06-02               North West     27
## 855   2020-06-03               North West     22
## 856   2020-06-04               North West     22
## 857   2020-06-05               North West     16
## 858   2020-06-06               North West     26
## 859   2020-06-07               North West     20
## 860   2020-06-08               North West     23
## 861   2020-06-09               North West     17
## 862   2020-06-10               North West     16
## 863   2020-06-11               North West     16
## 864   2020-06-12               North West     11
## 865   2020-06-13               North West     10
## 866   2020-06-14               North West     15
## 867   2020-06-15               North West     16
## 868   2020-06-16               North West     16
## 869   2020-06-17               North West     13
## 870   2020-06-18               North West     14
## 871   2020-06-19               North West      7
## 872   2020-06-20               North West     11
## 873   2020-06-21               North West      8
## 874   2020-06-22               North West     11
## 875   2020-06-23               North West     13
## 876   2020-06-24               North West     13
## 877   2020-06-25               North West     15
## 878   2020-06-26               North West      6
## 879   2020-06-27               North West      7
## 880   2020-06-28               North West      9
## 881   2020-06-29               North West      9
## 882   2020-06-30               North West      7
## 883   2020-07-01               North West      3
## 884   2020-07-02               North West      6
## 885   2020-07-03               North West      7
## 886   2020-07-04               North West      4
## 887   2020-07-05               North West      6
## 888   2020-07-06               North West      9
## 889   2020-07-07               North West      8
## 890   2020-07-08               North West      5
## 891   2020-07-09               North West     10
## 892   2020-07-10               North West      2
## 893   2020-07-11               North West      5
## 894   2020-07-12               North West      0
## 895   2020-07-13               North West      6
## 896   2020-07-14               North West      4
## 897   2020-07-15               North West      5
## 898   2020-07-16               North West      2
## 899   2020-07-17               North West      4
## 900   2020-07-18               North West      5
## 901   2020-07-19               North West      3
## 902   2020-07-20               North West      0
## 903   2020-07-21               North West      2
## 904   2020-07-22               North West      3
## 905   2020-07-23               North West      3
## 906   2020-07-24               North West      1
## 907   2020-07-25               North West      1
## 908   2020-07-26               North West      3
## 909   2020-07-27               North West      1
## 910   2020-07-28               North West      1
## 911   2020-07-29               North West      2
## 912   2020-07-30               North West      2
## 913   2020-07-31               North West      0
## 914   2020-08-01               North West      2
## 915   2020-08-02               North West      1
## 916   2020-08-03               North West      8
## 917   2020-08-04               North West      3
## 918   2020-08-05               North West      2
## 919   2020-08-06               North West      2
## 920   2020-08-07               North West      2
## 921   2020-08-08               North West      2
## 922   2020-08-09               North West      3
## 923   2020-08-10               North West      2
## 924   2020-08-11               North West      3
## 925   2020-08-12               North West      0
## 926   2020-08-13               North West      2
## 927   2020-08-14               North West      2
## 928   2020-08-15               North West      6
## 929   2020-08-16               North West      2
## 930   2020-08-17               North West      1
## 931   2020-08-18               North West      2
## 932   2020-08-19               North West      0
## 933   2020-08-20               North West      1
## 934   2020-08-21               North West      4
## 935   2020-08-22               North West      3
## 936   2020-08-23               North West      4
## 937   2020-08-24               North West      4
## 938   2020-08-25               North West      3
## 939   2020-08-26               North West      4
## 940   2020-08-27               North West      1
## 941   2020-08-28               North West      2
## 942   2020-08-29               North West      0
## 943   2020-08-30               North West      2
## 944   2020-08-31               North West      2
## 945   2020-09-01               North West      0
## 946   2020-09-02               North West      2
## 947   2020-09-03               North West      1
## 948   2020-09-04               North West      2
## 949   2020-09-05               North West      4
## 950   2020-09-06               North West      0
## 951   2020-03-01               South East      0
## 952   2020-03-02               South East      0
## 953   2020-03-03               South East      1
## 954   2020-03-04               South East      0
## 955   2020-03-05               South East      1
## 956   2020-03-06               South East      0
## 957   2020-03-07               South East      0
## 958   2020-03-08               South East      1
## 959   2020-03-09               South East      1
## 960   2020-03-10               South East      1
## 961   2020-03-11               South East      1
## 962   2020-03-12               South East      0
## 963   2020-03-13               South East      1
## 964   2020-03-14               South East      1
## 965   2020-03-15               South East      5
## 966   2020-03-16               South East      8
## 967   2020-03-17               South East      7
## 968   2020-03-18               South East     10
## 969   2020-03-19               South East      9
## 970   2020-03-20               South East     13
## 971   2020-03-21               South East      7
## 972   2020-03-22               South East     25
## 973   2020-03-23               South East     20
## 974   2020-03-24               South East     22
## 975   2020-03-25               South East     29
## 976   2020-03-26               South East     35
## 977   2020-03-27               South East     35
## 978   2020-03-28               South East     36
## 979   2020-03-29               South East     55
## 980   2020-03-30               South East     58
## 981   2020-03-31               South East     65
## 982   2020-04-01               South East     66
## 983   2020-04-02               South East     55
## 984   2020-04-03               South East     72
## 985   2020-04-04               South East     80
## 986   2020-04-05               South East     82
## 987   2020-04-06               South East     88
## 988   2020-04-07               South East    100
## 989   2020-04-08               South East     83
## 990   2020-04-09               South East    104
## 991   2020-04-10               South East     88
## 992   2020-04-11               South East     88
## 993   2020-04-12               South East     88
## 994   2020-04-13               South East     84
## 995   2020-04-14               South East     65
## 996   2020-04-15               South East     72
## 997   2020-04-16               South East     56
## 998   2020-04-17               South East     86
## 999   2020-04-18               South East     57
## 1000  2020-04-19               South East     70
## 1001  2020-04-20               South East     87
## 1002  2020-04-21               South East     51
## 1003  2020-04-22               South East     54
## 1004  2020-04-23               South East     57
## 1005  2020-04-24               South East     64
## 1006  2020-04-25               South East     51
## 1007  2020-04-26               South East     51
## 1008  2020-04-27               South East     41
## 1009  2020-04-28               South East     40
## 1010  2020-04-29               South East     47
## 1011  2020-04-30               South East     29
## 1012  2020-05-01               South East     37
## 1013  2020-05-02               South East     36
## 1014  2020-05-03               South East     17
## 1015  2020-05-04               South East     35
## 1016  2020-05-05               South East     29
## 1017  2020-05-06               South East     25
## 1018  2020-05-07               South East     27
## 1019  2020-05-08               South East     26
## 1020  2020-05-09               South East     28
## 1021  2020-05-10               South East     19
## 1022  2020-05-11               South East     25
## 1023  2020-05-12               South East     27
## 1024  2020-05-13               South East     18
## 1025  2020-05-14               South East     32
## 1026  2020-05-15               South East     25
## 1027  2020-05-16               South East     22
## 1028  2020-05-17               South East     18
## 1029  2020-05-18               South East     22
## 1030  2020-05-19               South East     12
## 1031  2020-05-20               South East     22
## 1032  2020-05-21               South East     15
## 1033  2020-05-22               South East     17
## 1034  2020-05-23               South East     21
## 1035  2020-05-24               South East     17
## 1036  2020-05-25               South East     13
## 1037  2020-05-26               South East     19
## 1038  2020-05-27               South East     19
## 1039  2020-05-28               South East     12
## 1040  2020-05-29               South East     22
## 1041  2020-05-30               South East      8
## 1042  2020-05-31               South East     12
## 1043  2020-06-01               South East     11
## 1044  2020-06-02               South East     13
## 1045  2020-06-03               South East     18
## 1046  2020-06-04               South East     11
## 1047  2020-06-05               South East     11
## 1048  2020-06-06               South East     10
## 1049  2020-06-07               South East     12
## 1050  2020-06-08               South East      8
## 1051  2020-06-09               South East     10
## 1052  2020-06-10               South East     11
## 1053  2020-06-11               South East      5
## 1054  2020-06-12               South East      6
## 1055  2020-06-13               South East      7
## 1056  2020-06-14               South East      7
## 1057  2020-06-15               South East      8
## 1058  2020-06-16               South East     14
## 1059  2020-06-17               South East      9
## 1060  2020-06-18               South East      4
## 1061  2020-06-19               South East      7
## 1062  2020-06-20               South East      5
## 1063  2020-06-21               South East      3
## 1064  2020-06-22               South East      2
## 1065  2020-06-23               South East      9
## 1066  2020-06-24               South East      7
## 1067  2020-06-25               South East      5
## 1068  2020-06-26               South East      8
## 1069  2020-06-27               South East      9
## 1070  2020-06-28               South East      6
## 1071  2020-06-29               South East      5
## 1072  2020-06-30               South East      5
## 1073  2020-07-01               South East      2
## 1074  2020-07-02               South East      8
## 1075  2020-07-03               South East      3
## 1076  2020-07-04               South East      6
## 1077  2020-07-05               South East      5
## 1078  2020-07-06               South East      4
## 1079  2020-07-07               South East      6
## 1080  2020-07-08               South East      3
## 1081  2020-07-09               South East      7
## 1082  2020-07-10               South East      3
## 1083  2020-07-11               South East      4
## 1084  2020-07-12               South East      4
## 1085  2020-07-13               South East      5
## 1086  2020-07-14               South East      5
## 1087  2020-07-15               South East      6
## 1088  2020-07-16               South East      3
## 1089  2020-07-17               South East      1
## 1090  2020-07-18               South East      5
## 1091  2020-07-19               South East      2
## 1092  2020-07-20               South East      6
## 1093  2020-07-21               South East      4
## 1094  2020-07-22               South East      2
## 1095  2020-07-23               South East      3
## 1096  2020-07-24               South East      1
## 1097  2020-07-25               South East      1
## 1098  2020-07-26               South East      3
## 1099  2020-07-27               South East      1
## 1100  2020-07-28               South East      3
## 1101  2020-07-29               South East      2
## 1102  2020-07-30               South East      3
## 1103  2020-07-31               South East      1
## 1104  2020-08-01               South East      2
## 1105  2020-08-02               South East      4
## 1106  2020-08-03               South East      0
## 1107  2020-08-04               South East      0
## 1108  2020-08-05               South East      0
## 1109  2020-08-06               South East      2
## 1110  2020-08-07               South East      0
## 1111  2020-08-08               South East      2
## 1112  2020-08-09               South East      0
## 1113  2020-08-10               South East      2
## 1114  2020-08-11               South East      1
## 1115  2020-08-12               South East      1
## 1116  2020-08-13               South East      0
## 1117  2020-08-14               South East      0
## 1118  2020-08-15               South East      2
## 1119  2020-08-16               South East      1
## 1120  2020-08-17               South East      0
## 1121  2020-08-18               South East      2
## 1122  2020-08-19               South East      1
## 1123  2020-08-20               South East      0
## 1124  2020-08-21               South East      0
## 1125  2020-08-22               South East      0
## 1126  2020-08-23               South East      1
## 1127  2020-08-24               South East      0
## 1128  2020-08-25               South East      1
## 1129  2020-08-26               South East      0
## 1130  2020-08-27               South East      0
## 1131  2020-08-28               South East      1
## 1132  2020-08-29               South East      0
## 1133  2020-08-30               South East      0
## 1134  2020-08-31               South East      2
## 1135  2020-09-01               South East      1
## 1136  2020-09-02               South East      1
## 1137  2020-09-03               South East      0
## 1138  2020-09-04               South East      0
## 1139  2020-09-05               South East      0
## 1140  2020-09-06               South East      0
## 1141  2020-03-01               South West      0
## 1142  2020-03-02               South West      0
## 1143  2020-03-03               South West      0
## 1144  2020-03-04               South West      0
## 1145  2020-03-05               South West      0
## 1146  2020-03-06               South West      0
## 1147  2020-03-07               South West      0
## 1148  2020-03-08               South West      0
## 1149  2020-03-09               South West      0
## 1150  2020-03-10               South West      0
## 1151  2020-03-11               South West      1
## 1152  2020-03-12               South West      0
## 1153  2020-03-13               South West      0
## 1154  2020-03-14               South West      1
## 1155  2020-03-15               South West      0
## 1156  2020-03-16               South West      0
## 1157  2020-03-17               South West      2
## 1158  2020-03-18               South West      2
## 1159  2020-03-19               South West      4
## 1160  2020-03-20               South West      3
## 1161  2020-03-21               South West      6
## 1162  2020-03-22               South West      7
## 1163  2020-03-23               South West      8
## 1164  2020-03-24               South West      7
## 1165  2020-03-25               South West      9
## 1166  2020-03-26               South West     11
## 1167  2020-03-27               South West     13
## 1168  2020-03-28               South West     21
## 1169  2020-03-29               South West     18
## 1170  2020-03-30               South West     23
## 1171  2020-03-31               South West     23
## 1172  2020-04-01               South West     21
## 1173  2020-04-02               South West     23
## 1174  2020-04-03               South West     30
## 1175  2020-04-04               South West     42
## 1176  2020-04-05               South West     32
## 1177  2020-04-06               South West     34
## 1178  2020-04-07               South West     39
## 1179  2020-04-08               South West     47
## 1180  2020-04-09               South West     24
## 1181  2020-04-10               South West     46
## 1182  2020-04-11               South West     43
## 1183  2020-04-12               South West     23
## 1184  2020-04-13               South West     27
## 1185  2020-04-14               South West     24
## 1186  2020-04-15               South West     32
## 1187  2020-04-16               South West     29
## 1188  2020-04-17               South West     33
## 1189  2020-04-18               South West     25
## 1190  2020-04-19               South West     31
## 1191  2020-04-20               South West     26
## 1192  2020-04-21               South West     26
## 1193  2020-04-22               South West     23
## 1194  2020-04-23               South West     17
## 1195  2020-04-24               South West     19
## 1196  2020-04-25               South West     15
## 1197  2020-04-26               South West     27
## 1198  2020-04-27               South West     13
## 1199  2020-04-28               South West     17
## 1200  2020-04-29               South West     15
## 1201  2020-04-30               South West     26
## 1202  2020-05-01               South West      6
## 1203  2020-05-02               South West      7
## 1204  2020-05-03               South West     10
## 1205  2020-05-04               South West     17
## 1206  2020-05-05               South West     14
## 1207  2020-05-06               South West     19
## 1208  2020-05-07               South West     16
## 1209  2020-05-08               South West      6
## 1210  2020-05-09               South West     11
## 1211  2020-05-10               South West      5
## 1212  2020-05-11               South West      8
## 1213  2020-05-12               South West      7
## 1214  2020-05-13               South West      7
## 1215  2020-05-14               South West      6
## 1216  2020-05-15               South West      4
## 1217  2020-05-16               South West      4
## 1218  2020-05-17               South West      6
## 1219  2020-05-18               South West      4
## 1220  2020-05-19               South West      6
## 1221  2020-05-20               South West      1
## 1222  2020-05-21               South West      9
## 1223  2020-05-22               South West      7
## 1224  2020-05-23               South West      6
## 1225  2020-05-24               South West      3
## 1226  2020-05-25               South West      8
## 1227  2020-05-26               South West     11
## 1228  2020-05-27               South West      5
## 1229  2020-05-28               South West     10
## 1230  2020-05-29               South West      7
## 1231  2020-05-30               South West      3
## 1232  2020-05-31               South West      2
## 1233  2020-06-01               South West      7
## 1234  2020-06-02               South West      2
## 1235  2020-06-03               South West      7
## 1236  2020-06-04               South West      2
## 1237  2020-06-05               South West      2
## 1238  2020-06-06               South West      1
## 1239  2020-06-07               South West      3
## 1240  2020-06-08               South West      3
## 1241  2020-06-09               South West      0
## 1242  2020-06-10               South West      1
## 1243  2020-06-11               South West      2
## 1244  2020-06-12               South West      2
## 1245  2020-06-13               South West      2
## 1246  2020-06-14               South West      0
## 1247  2020-06-15               South West      2
## 1248  2020-06-16               South West      2
## 1249  2020-06-17               South West      0
## 1250  2020-06-18               South West      0
## 1251  2020-06-19               South West      0
## 1252  2020-06-20               South West      2
## 1253  2020-06-21               South West      0
## 1254  2020-06-22               South West      1
## 1255  2020-06-23               South West      1
## 1256  2020-06-24               South West      1
## 1257  2020-06-25               South West      0
## 1258  2020-06-26               South West      3
## 1259  2020-06-27               South West      0
## 1260  2020-06-28               South West      0
## 1261  2020-06-29               South West      1
## 1262  2020-06-30               South West      0
## 1263  2020-07-01               South West      0
## 1264  2020-07-02               South West      0
## 1265  2020-07-03               South West      0
## 1266  2020-07-04               South West      0
## 1267  2020-07-05               South West      1
## 1268  2020-07-06               South West      0
## 1269  2020-07-07               South West      0
## 1270  2020-07-08               South West      2
## 1271  2020-07-09               South West      0
## 1272  2020-07-10               South West      1
## 1273  2020-07-11               South West      0
## 1274  2020-07-12               South West      0
## 1275  2020-07-13               South West      1
## 1276  2020-07-14               South West      0
## 1277  2020-07-15               South West      0
## 1278  2020-07-16               South West      0
## 1279  2020-07-17               South West      1
## 1280  2020-07-18               South West      0
## 1281  2020-07-19               South West      0
## 1282  2020-07-20               South West      0
## 1283  2020-07-21               South West      0
## 1284  2020-07-22               South West      0
## 1285  2020-07-23               South West      0
## 1286  2020-07-24               South West      0
## 1287  2020-07-25               South West      0
## 1288  2020-07-26               South West      0
## 1289  2020-07-27               South West      0
## 1290  2020-07-28               South West      0
## 1291  2020-07-29               South West      0
## 1292  2020-07-30               South West      1
## 1293  2020-07-31               South West      0
## 1294  2020-08-01               South West      0
## 1295  2020-08-02               South West      0
## 1296  2020-08-03               South West      0
## 1297  2020-08-04               South West      0
## 1298  2020-08-05               South West      0
## 1299  2020-08-06               South West      0
## 1300  2020-08-07               South West      0
## 1301  2020-08-08               South West      0
## 1302  2020-08-09               South West      0
## 1303  2020-08-10               South West      0
## 1304  2020-08-11               South West      0
## 1305  2020-08-12               South West      0
## 1306  2020-08-13               South West      0
## 1307  2020-08-14               South West      1
## 1308  2020-08-15               South West      0
## 1309  2020-08-16               South West      0
## 1310  2020-08-17               South West      2
## 1311  2020-08-18               South West      0
## 1312  2020-08-19               South West      0
## 1313  2020-08-20               South West      0
## 1314  2020-08-21               South West      0
## 1315  2020-08-22               South West      0
## 1316  2020-08-23               South West      0
## 1317  2020-08-24               South West      0
## 1318  2020-08-25               South West      1
## 1319  2020-08-26               South West      0
## 1320  2020-08-27               South West      1
## 1321  2020-08-28               South West      0
## 1322  2020-08-29               South West      0
## 1323  2020-08-30               South West      0
## 1324  2020-08-31               South West      0
## 1325  2020-09-01               South West      0
## 1326  2020-09-02               South West      0
## 1327  2020-09-03               South West      0
## 1328  2020-09-04               South West      0
## 1329  2020-09-05               South West      0
## 1330  2020-09-06               South West      0

1.5 Completion date

We extract the completion date from the NHS Pathways file timestamp:


database_date <- attr(x, "timestamp")
database_date
## [1] "2020-09-07"

The completion date of the NHS Pathways data is Monday 07 Sep 2020.

1.6 Auxiliary functions

These are functions which will be used further in the analyses.

Function to estimate the generalised R-squared as the proportion of deviance explained by a given model:


## Function to calculate R2 for Poisson model
## not adjusted for model complexity but all models have the same DF here

Rsq <- function(x) {
  1 - (x$deviance / x$null.deviance)
}

Function to extract growth rates per region as well as halving times, and the associated 95% confidence intervals:


## function to extract the coefficients, find the level of the intercept,
## reconstruct the values of r, get confidence intervals

get_r <- function(model) {
  ##  extract coefficients and conf int
  out <- data.frame(r = coef(model))  %>%
    rownames_to_column("var") %>% 
    cbind(confint(model)) %>%
    filter(!grepl("day_of_week", var)) %>% 
    filter(grepl("day", var)) %>%
    rename(lower_95 = "2.5 %",
           upper_95 = "97.5 %") %>%
    mutate(var = sub("day:", "", var))
  
  ## reconstruct values: intercept + region-coefficient
  for (i in 2:nrow(out)) {
    out[i, -1] <- out[1, -1] + out[i, -1]
  }
  
  ## find the name of the intercept, restore regions names
  out <- out %>%
    mutate(nhs_region = model$xlevels$nhs_region) %>%
    select(nhs_region, everything(), -var)
  
  ## find halving times
  halving <- log(0.5) / out[,-1] %>%
    rename(halving_t = r,
           halving_t_lower_95 = lower_95,
           halving_t_upper_95 = upper_95)
  
  ## set halving times with exclusion intervals to NA
  no_halving <- out$lower_95 < 0 & out$upper_95 > 0
  halving[no_halving, ] <- NA_real_
  
  ## return all data
  cbind(out, halving)
  
}

Functions used in the correlation analysis between NHS Pathways reports and deaths:

## Function to calculate Pearson's correlation between deaths and lagged
## reports. Note that `pearson` can be replaced with `spearman` for rank
## correlation.

getcor <- function(x, ndx) {
  return(cor(x$deaths[ndx],
             x$note_lag[ndx],
             use = "complete.obs",
             method = "pearson"))
}

## Catch if sample size throws an error
getcor2 <- possibly(getcor, otherwise = NA)

getboot <- function(x) {
  result <- boot::boot.ci(boot::boot(x, getcor2, R = 1000), 
                           type = "bca")
  return(data.frame(n = sum(!is.na(x$note_lag) & !is.na(x$deaths)),
                    r = result$t0,
                    r_low = result$bca[4],
                    r_hi = result$bca[5]))
}

Function to classify the day of the week into weekend, Monday, and the rest:


## Fn to add day of week
day_of_week <- function(df) {
  df %>% 
    dplyr::mutate(day_of_week = lubridate::wday(date, label = TRUE)) %>% 
    dplyr::mutate(day_of_week = dplyr::case_when(
      day_of_week %in% c("Sat", "Sun") ~ "weekend",
      day_of_week %in% c("Mon") ~ "monday",
      !(day_of_week %in% c("Sat", "Sun", "Mon")) ~ "rest_of_week"
    ) %>% 
      factor(levels = c("rest_of_week", "monday", "weekend")))
}

Custom color palettes, color scales, and vectors of colors:


pal <- c("#006212",
         "#ae3cab",
         "#00db90",
         "#960c00",
         "#55aaff",
         "#ff7e78",
         "#00388d")

age.pal <- viridis::viridis(3,begin = 0.1, end = 0.7)

3 Comparison with deaths time series

3.1 Outline

We want to explore the correlation between NHS Pathways reports and deaths, and assess the potential for reports to be used as an early warning system for disease resurgence.

Death data are publically available. We truncate the time series to avoid bias from reporting delay - we assume a conservative delay of three weeks.

3.2 Lagged correlation

We calculate Pearson’s correlation coefficient between deaths and NHS Pathways notifications using different lags. Confidence intervals are obtained using bootstrap. Note that results were also confirmed using Spearman’s rank correlation.

First we join the NHS Pathways and death data, and aggregate over all England:

## truncate death data for reporting delay
trunc_date <- max(dth$date_report) - delay_max

dth_trunc <- dth %>%
  rename(date = date_report) %>%
  filter(date <= trunc_date) 

## join with notification data
all_data <- x %>% 
  filter(!is.na(nhs_region)) %>%
  group_by(date, nhs_region) %>%
  summarise(count = sum(count, na.rm = T)) %>%
  ungroup %>%
  inner_join(dth_trunc,
             by = c("date","nhs_region"))

all_tot <- all_data %>%
  group_by(date) %>%
  summarise(count = sum(count, na.rm = TRUE),
            deaths = sum(deaths, na.rm = TRUE)) 

We calculate correlation with lagged NHS Pathways reports from 0 to 30 days behind deaths:


## Calculate all correlations + bootstrap CIs
lag_cor <- data.frame()
for (i in 0:30) {
  
  ## lag reports
  summary <- all_tot %>% 
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI
    getboot(.) %>%
    mutate(lag = i)

  lag_cor <- bind_rows(lag_cor, summary)
}

cor_vs_lag <- ggplot(lag_cor, aes(lag, r)) +
  theme_bw() +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi), alpha = 0.2) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_point() +
  geom_line() +
  labs(x = "Lag between NHS pathways and death data (days)",
       y = "Pearson's correlation") +
  large_txt
cor_vs_lag


l_opt <- which.max(lag_cor$r)

This analysis suggests that the best lag is 23 days. We then compare and plot the number of deaths reported against the number of NHS Pathways reports lagged by 23 days.


all_tot <- all_tot %>%
  rename(date_death = date) %>%
  mutate(note_lag = lag(count, lag_cor$lag[l_opt]),
         note_lag_c = (note_lag - mean(note_lag, na.rm = T)),
         date_note = lag(date_death,16))

lag_mod <- glm(deaths ~ note_lag, data = all_tot, family = "quasipoisson")

summary(lag_mod)
## 
## Call:
## glm(formula = deaths ~ note_lag, family = "quasipoisson", data = all_tot)
## 
## Deviance Residuals: 
##     Min       1Q   Median       3Q      Max  
## -19.183   -7.760   -2.822    4.313   12.814  
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)    
## (Intercept) 4.075e+00  8.202e-02   49.68   <2e-16 ***
## note_lag    1.881e-05  8.525e-07   22.06   <2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for quasipoisson family taken to be 47.3338)
## 
##     Null deviance: 26212.4  on 128  degrees of freedom
## Residual deviance:  6510.8  on 127  degrees of freedom
##   (23 observations deleted due to missingness)
## AIC: NA
## 
## Number of Fisher Scoring iterations: 5

exp(coefficients(lag_mod))
## (Intercept)    note_lag 
##   58.840206    1.000019
exp(confint(lag_mod))
##                 2.5 %   97.5 %
## (Intercept) 49.920888 68.86170
## note_lag     1.000017  1.00002

Rsq(lag_mod)
## [1] 0.7516134

mod_fit <- as.data.frame(predict(lag_mod, type = "link", se.fit = TRUE)[1:2])

all_tot_pred <- 
  all_tot %>%
  filter(!is.na(note_lag)) %>%
  mutate(pred = mod_fit$fit,
         pred.se = mod_fit$se.fit,
         low = exp(pred - 1.96*pred.se),
         hi = exp(pred + 1.96*pred.se))


glm_fit <- all_tot_pred %>% 
    filter(!is.na(note_lag)) %>%
  ggplot(aes(x = note_lag, y = deaths)) +
  geom_point() + 
  geom_line(aes(y = exp(pred))) + 
  geom_ribbon(aes(ymin = low, ymax = hi), alpha = 0.3, col = "grey") +
  theme_bw() +
  labs(y = "Daily number of\ndeaths reported",
       x = "Daily number of NHS Pathways reports") +
  large_txt

glm_fit

4 Supplementary figures

4.1 Serial interval distribution

This is a comparison of gamma versus lognormal distribution for the serial interval used to convert r to R in our analysis. Both distributions are parameterised with mean 4.7 and standard deviation 2.9.

SI_param <- epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale, w = 0.5)

SI_distribution2 <- distcrete::distcrete("lnorm", interval = 1,
                                        meanlog = log(4.7),
                                        sdlog = log(2.9), w = 0.5)

SI_dist1 <- data.frame(x = SI_distribution$r(1e5)) 
SI_dist1 <- count(SI_dist1, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 30, 5)) +
    theme_bw()

SI_dist2 <- data.frame(x = SI_distribution2$r(1e5)) 
SI_dist2 <- count(SI_dist2, x) %>%
    ggplot() +
    geom_col(aes(x = x, y = n)) +
    labs(x = "Serial interval (days)", y = "Frequency") +
    scale_x_continuous(breaks = seq(0, 200, 20), limits = c(0, 200)) +
    theme_bw()


ggpubr::ggarrange(SI_dist1,
                  SI_dist2,
                  nrow = 1,
                  labels = "AUTO") 

4.2 Sensitivity analysis - 7 or 21 days moving window

We reproduce the window analysis with either a 7 or 21 days window for sensitivity purposes.

First with the 7 days window:

## set moving time window (1/2/3 weeks)
w <- 7

# create empty df
r_all_sliding_7days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_7days <- bind_rows(r_all_sliding_7days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_7days <- r_all_sliding_7days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
plot_R <- r_all_sliding_7days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_7days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_7days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_7 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

Then with the 21 days window:

## set moving time window (1/2/3 weeks)
w <- 21

# create empty df
r_all_sliding_21days <- NULL

## make data for model
x_model_all_moving <- x %>%
  filter(!is.na(nhs_region)) %>% 
  group_by(date, nhs_region) %>%
  summarise(n = sum(count)) 

unique_dates <- unique(x_model_all_moving$date)

for (i in 1:(length(unique_dates) - w)) {
  
  date_i <- unique_dates[i]
  
  date_i_max <- date_i + w
  
  model_data <- x_model_all_moving %>%
    filter(date >= date_i & date < date_i_max) %>%
    mutate(day = as.integer(date - date_i)) %>% 
    day_of_week()
  
  
  mod <- glm(n ~ day * nhs_region + day_of_week,
             data = model_data,
             family = 'quasipoisson')
  
  # get growth rate
  r <- get_r(mod)
  r$w_min <- date_i
  r$w_max <- date_i_max
  
  # combine all estimates
  r_all_sliding_21days <- bind_rows(r_all_sliding_21days, r)
  
}

#serial interval distribution
SI_param = epitrix::gamma_mucv2shapescale(4.7, 2.9/4.7)
SI_distribution <- distcrete::distcrete("gamma", interval = 1,
                                        shape = SI_param$shape,
                                        scale = SI_param$scale,
                                        w = 0.5)

#convert growth rates r to R0
r_all_sliding_21days <- r_all_sliding_21days %>%
  mutate(R = epitrix::r2R0(r, SI_distribution),
         R_lower_95 = epitrix::r2R0(lower_95, SI_distribution),
         R_upper_95 = epitrix::r2R0(upper_95, SI_distribution))
# plot
plot_growth <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = r)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 0, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(colour = guide_legend(title = "",override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated daily growth rate (r)") +
  scale_colour_manual(values = pal)
# plot
plot_R <-
  r_all_sliding_21days %>%
  ggplot(aes(x = w_max, y = R)) +
  geom_ribbon(aes(ymin = R_lower_95, ymax = R_upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(yintercept = 1, linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0.5,0.5, "cm")) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "",
       y = "Estimated effective reproduction\nnumber (Re)") +
  scale_colour_manual(values = pal)

R <- r_all_sliding_21days %>%
  mutate(lower_95 = R_lower_95, 
         upper_95 = R_upper_95,
         value = R,
         measure = "R",
         reference = 1)

r_R <- r_all_sliding_21days %>%
  mutate(measure = "r",
         value = r,
         reference = 0) %>%
  bind_rows(R)

r_R_21 <- r_R %>%
  ggplot(aes(x = w_max, y = value)) +
  geom_ribbon(aes(ymin = lower_95, ymax = upper_95, fill = nhs_region), alpha = 0.1) +
  geom_line(aes(colour = nhs_region)) +
  geom_point(aes(colour = nhs_region)) +
  geom_hline(aes(yintercept = reference), linetype = "dashed") +
  theme_bw() +
  scale_weeks +
  theme(legend.position = "bottom",
        plot.margin = margin(0.5,1,0,0, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside"
  ) +
  guides(color = guide_legend(title = "", override.aes = list(fill = NA)), fill = FALSE) +
  labs(x = "", y = "") +
  scale_colour_manual(values = pal) +
  facet_grid(rows = vars(measure),
             scales = "free_y",
             switch = "y",
             labeller = as_labeller(c(r = "Daily growth rate (r)",
                                      R = "Effective reproduction\nnumber (Re)")))

And we combine both outputs into a single plot:


ggpubr::ggarrange(r_R_7,
                  r_R_21,
                  nrow = 2,
                  labels = "AUTO",
                  common.legend = TRUE,
                  legend = "bottom") 

4.3 Correlation between NHS Pathways reports and deaths by NHS region


lag_cor_reg <- data.frame()

for (i in 0:30) {

  summary <-
    all_data %>%
    group_by(nhs_region) %>%
    mutate(note_lag = lag(count, i)) %>%
    ## calculate rank correlation and bootstrap CI for each region
    group_modify(~getboot(.x)) %>%
    mutate(lag = i)
  
  lag_cor_reg <- bind_rows(lag_cor_reg, summary)
}

cor_vs_lag_reg <- 
lag_cor_reg %>%
ggplot(aes(lag, r, col = nhs_region)) +
  geom_hline(yintercept = 0, lty = "longdash") +
  geom_ribbon(aes(ymin = r_low, ymax = r_hi, col = NULL, fill = nhs_region), alpha = 0.2) +
  geom_point() +
  geom_line() +
  facet_wrap(~nhs_region) +
  scale_color_manual(values = pal) +
  scale_fill_manual(values = pal, guide = F) +  
  theme_bw() +
  labs(x = "Lag between NHS pathways and death data (days)", y = "Pearson's correlation", col = "NHS region") +
  theme(legend.position = "bottom") +
  guides(color = guide_legend(override.aes = list(fill = NA)))

cor_vs_lag_reg

5 Export data

We save the tables created during our analysis:


if (!dir.exists("excel_tables")) {
  dir.create("excel_tables")
}


## list all tables, and loop over export
tables_to_export <- c("r_all_sliding", "lag_cor")

for (e in tables_to_export) {
  rio::export(get(e),
              file.path("excel_tables",
                        paste0(e, ".xlsx")))
}

## also export result from regression on lagged data 
rio::export(lag_mod, file.path("excel_tables", "lag_mod.rds"))

6 System information

6.1 Outline

The following information documents the system on which the document was compiled.

6.2 System

This provides information on the operating system.

Sys.info()
##                                                                                            sysname 
##                                                                                           "Darwin" 
##                                                                                            release 
##                                                                                           "19.6.0" 
##                                                                                            version 
## "Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64" 
##                                                                                           nodename 
##                                                                                   "Mac-1758.local" 
##                                                                                            machine 
##                                                                                           "x86_64" 
##                                                                                              login 
##                                                                                             "root" 
##                                                                                               user 
##                                                                                           "runner" 
##                                                                                     effective_user 
##                                                                                           "runner"

6.3 R environment

This provides information on the version of R used:

R.version
##                _                           
## platform       x86_64-apple-darwin17.0     
## arch           x86_64                      
## os             darwin17.0                  
## system         x86_64, darwin17.0          
## status                                     
## major          4                           
## minor          0.2                         
## year           2020                        
## month          06                          
## day            22                          
## svn rev        78730                       
## language       R                           
## version.string R version 4.0.2 (2020-06-22)
## nickname       Taking Off Again

6.4 R packages

This provides information on the packages used:

sessionInfo()
## R version 4.0.2 (2020-06-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.6
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ggnewscale_0.4.3     ggpubr_0.4.0         lubridate_1.7.9     
##  [4] chngpt_2020.8-29     cyphr_1.1.0          DT_0.15             
##  [7] kableExtra_1.2.1     janitor_2.0.1        remotes_2.2.0       
## [10] projections_0.5.1    earlyR_0.0.1         epitrix_0.2.2       
## [13] distcrete_1.0.3      incidence_1.7.2      rio_0.5.16          
## [16] reshape2_1.4.4       rvest_0.3.6          xml2_1.3.2          
## [19] linelist_0.0.40.9000 forcats_0.5.0        stringr_1.4.0       
## [22] dplyr_1.0.2          purrr_0.3.4          readr_1.3.1         
## [25] tidyr_1.1.2          tibble_3.0.3         ggplot2_3.3.2       
## [28] tidyverse_1.3.0      here_0.1             reportfactory_0.0.5 
## 
## loaded via a namespace (and not attached):
##  [1] minqa_1.2.4       colorspace_1.4-1  selectr_0.4-2     ggsignif_0.6.0   
##  [5] ellipsis_0.3.1    rprojroot_1.3-2   snakecase_0.11.0  fs_1.5.0         
##  [9] rstudioapi_0.11   farver_2.0.3      fansi_0.4.1       splines_4.0.2    
## [13] knitr_1.29        jsonlite_1.7.1    nloptr_1.2.2.2    broom_0.7.0      
## [17] dbplyr_1.4.4      compiler_4.0.2    httr_1.4.2        backports_1.1.9  
## [21] assertthat_0.2.1  Matrix_1.2-18     cli_2.0.2         htmltools_0.5.0  
## [25] tools_4.0.2       gtable_0.3.0      glue_1.4.2        Rcpp_1.0.5       
## [29] carData_3.0-4     cellranger_1.1.0  vctrs_0.3.4       nlme_3.1-148     
## [33] matchmaker_0.1.1  crosstalk_1.1.0.1 xfun_0.16         openxlsx_4.1.5   
## [37] lme4_1.1-23       lifecycle_0.2.0   statmod_1.4.34    rstatix_0.6.0    
## [41] MASS_7.3-51.6     scales_1.1.1      hms_0.5.3         sodium_1.1       
## [45] yaml_2.2.1        curl_4.3          gridExtra_2.3     stringi_1.4.6    
## [49] kyotil_2020.8-22  boot_1.3-25       zip_2.1.1         rlang_0.4.7      
## [53] pkgconfig_2.0.3   evaluate_0.14     lattice_0.20-41   htmlwidgets_1.5.1
## [57] labeling_0.3      cowplot_1.1.0     tidyselect_1.1.0  plyr_1.8.6       
## [61] magrittr_1.5      R6_2.4.1          generics_0.0.2    DBI_1.1.0        
## [65] pillar_1.4.6      haven_2.3.1       foreign_0.8-80    withr_2.2.0      
## [69] mgcv_1.8-31       survival_3.1-12   abind_1.4-5       modelr_0.1.8     
## [73] crayon_1.3.4      car_3.0-9         utf8_1.1.4        rmarkdown_2.3    
## [77] viridis_0.5.1     grid_4.0.2        readxl_1.3.1      data.table_1.13.0
## [81] blob_1.2.1        reprex_0.3.0      digest_0.6.25     webshot_0.5.2    
## [85] munsell_0.5.0     viridisLite_0.3.0